Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

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dc.citation.articleNumbere1007872en_US
dc.citation.issueNumber12en_US
dc.citation.journalTitlePLoS Geneticsen_US
dc.citation.volumeNumber14en_US
dc.contributor.authorNir, Guyen_US
dc.contributor.authorFarabella, Ireneen_US
dc.contributor.authorEstrada, Cynthia Pérezen_US
dc.contributor.authorEbeling, Carl G.en_US
dc.contributor.authorBeliveau, Brian J.en_US
dc.contributor.authorSasaki, Hiroshi M.en_US
dc.contributor.authorLee, S. Deanen_US
dc.contributor.authorNguyen, Son C.en_US
dc.contributor.authorMcCole, Ruth B.en_US
dc.contributor.authorChattoraj, Shyamtanuen_US
dc.contributor.authorErceg, Jelenaen_US
dc.contributor.authorAbed, Jumana AlHajen_US
dc.contributor.authorMartins, Nuno M.C.en_US
dc.contributor.authorNguyen, Huy Q.en_US
dc.contributor.authorHannan, Mohammed A.en_US
dc.contributor.authorRussell, Sheikhen_US
dc.contributor.authorDurand, Neva C.en_US
dc.contributor.authorRao, Suhas S.P.en_US
dc.contributor.authorKishi, Jocelyn Y.en_US
dc.contributor.authorSoler-Vila, Paulaen_US
dc.contributor.authorPierro, Michele Dien_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.authorCallahan, Steven P.en_US
dc.contributor.authorSchreiner, John M.en_US
dc.contributor.authorStuckey, Jeff A.en_US
dc.contributor.authorYin, Pengen_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.authorMarti-Renom, Marc A.en_US
dc.contributor.authorWu, C.-tingen_US
dc.date.accessioned2019-01-24T16:08:02Zen_US
dc.date.available2019-01-24T16:08:02Zen_US
dc.date.issued2018en_US
dc.description.abstractChromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.en_US
dc.identifier.citationNir, Guy, Farabella, Irene, Estrada, Cynthia Pérez, et al.. "Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling." <i>PLoS Genetics,</i> 14, no. 12 (2018) Public Library of Science: https://doi.org/10.1371/journal.pgen.1007872.en_US
dc.identifier.digitaljournal-pgen-1007872en_US
dc.identifier.doihttps://doi.org/10.1371/journal.pgen.1007872en_US
dc.identifier.urihttps://hdl.handle.net/1911/105128en_US
dc.language.isoengen_US
dc.publisherPublic Library of Scienceen_US
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleWalking along chromosomes with super-resolution imaging, contact maps, and integrative modelingen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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